Invasive group A streptococcal disease surveillance in Canada, 2021–2022

Background Invasive group A streptococcal (iGAS, Streptococcus pyogenes) disease has been a nationally notifiable disease in Canada since 2000. This report summarizes the demographics, emm types, and antimicrobial resistance of iGAS isolates collected in Canada in 2021 and 2022. Methods The Public Health Agency of Canada’s National Microbiology Laboratory collaborates with provincial and territorial public health laboratories to conduct national surveillance of invasive S. pyogenes. Emm typing was performed using the Centers for Disease Control and Prevention emm sequencing protocol or extracted from whole-genome sequencing data. Antimicrobial susceptibilities were determined using Kirby-Bauer disk diffusion according to Clinical and Laboratory Standards Institute guidelines or predicted from whole-genome sequencing data based on the presence of resistance determinants. Results Overall, the incidence of iGAS disease in Canada was 5.56 cases per 100,000 population in 2021, decreasing from the peak of 8.6 cases per 100,000 population in 2018. A total of 2,630 iGAS isolates were collected during 2022, representing an increase from 2021 (n=2,179). In particular, there was a large increase in isolates collected from October to December 2022. The most predominant emm type overall in 2021 and 2022 was emm49, at 21.5% (n=468) and 16.9% (n=444), respectively, representing a significant increase in prevalence since 2018 (p<0.0001). The former most prevalent type, emm1, increased from 0.5% (n=10) in 2021 to 4.8% (n=125) in 2022; similarly, emm12 increased from 1.0% (n=22) in 2021 to 5.8% (n=151) in 2022. These two types together accounted for almost 25% of isolates collected in late 2022 (October to December). Antimicrobial resistance rates in 2021 and 2022 included: 14.9%/14.1% erythromycin resistance, 4.8%/3.0% clindamycin resistance, and <1% chloramphenicol resistance. Conclusion The increase of iGAS isolates collected in Canada is an important public health concern. Continued surveillance of iGAS is critical to monitor expanding emm types and antimicrobial resistance patterns.


Introduction
Invasive group A Streptococcus (iGAS, Streptococcus pyogenes) is responsible for a wide range of human diseases, the most serious of which include bacteraemia, streptococcal toxic shock syndrome, necrotizing fasciitis, and endocarditis (1).In Canada, the overall incidence of iGAS infections has steadily increased since becoming a notifiable disease in 2000, peaking at a rate of 8.61 cases per 100,000 population in 2018 (2).In 2020, Canada reported decreased submissions of iGAS isolates, attributed to the containment measures put in place to control the SARS-CoV-2 pandemic (COVID-19) (2).There was also a significant shift in the emm types most commonly associated with disease in Canada, shifting from the formerly prevalent emm1 toward emm49 and emm76 (2).
In late 2022, the World Health Organization (WHO) reported that several countries in Europe had been observing increased cases of iGAS and scarlet fever, predominantly in children (3), starting off a season of increased focus on iGAS in many countries.As COVID-19 pandemic restrictions have loosened and personto-person disease transmission has intensified, it is increasingly important to monitor the prevalence of both iGAS disease and associated emm types and antimicrobial resistance.This report provides a summary of iGAS isolates collected in Canada in 2021 and 2022.

Surveillance program
As previously described, surveillance of iGAS in Canada consists of a passive, laboratory-based system where invasive S. pyogenes isolates from all provincial and territorial public health laboratories (except Alberta) are forwarded to the National Microbiology Laboratory (NML) in Winnipeg for further testing (2).In 2021, a total of 2,179 iGAS isolates were reported, including 1,787 submitted directly to NML by provincial and territorial public health laboratories, as well as data for a further 392 isolates collected and tested by the Provincial Laboratory for Public Health in Edmonton, Alberta (ProvLab Alberta); in 2022, a total of 2,630 iGAS isolates were reported, including 2,108 submitted directly and data for 522 tested by ProvLab Alberta (Table 1).Sterile clinical isolation sites include blood, cerebrospinal fluid, deep tissue, biopsy and surgical samples, bone, and any clinical sources associated with necrotizing fasciitis or toxic shock syndrome.
Population-based incidences of iGAS disease up to 2021 were obtained through the Canadian Notifiable Disease Surveillance System (CNDSS).Population data for incidence rates were obtained from Statistics Canada's July 1 st , 2021, annual population estimates.

Results
After peaking at 8.61 cases per 100,000 population in 2018, the overall incidence of iGAS disease in Canada decreased in 2020 and 2021.The overall incidence rate in 2021 was 5.56 cases per 100,000 population, which is the lowest overall incidence in Canada since 2015 (Figure 1, Appendix, Supplemental Table S1).There was an increase in the number of iGAS isolates submitted in 2022 (n=2,630) in comparison to 2021 (n=2,179).In particular, there was a large increase in isolates collected in the final quarter (Q4; October to December) of 2022 (Figure 2), the total of which was considerably higher than Q4 in 2018 and 2019 (pre-pandemic years

Discussion
In 2021, 2,127 cases of iGAS were reported to CNDSS, with a national incidence rate of 5.56 cases per 100,000 population, a considerably lower rate than the peak seen in 2018 (8.61 cases per 100,000 population).This low incidence in 2021 is consistent with the lower rate seen in 2020 (6.85 cases per 100,000 population) and can likely be attributed to indirect effects of the containment measures put in place in 2020 to prevent the spread of the SARS-CoV-2 pandemic virus (COVID-19).Numerous studies have observed that invasive bacterial disease activity due to pathogens transmitted by respiratory droplets (including S. pyogenes) decreased during this time (2,(8)(9)(10).
Beginning in 2022, many countries began to see levels of iGAS disease increase once again.In December 2022, the WHO reported that five European countries had been observing increased cases of iGAS and scarlet fever, predominantly in children (3).Subsequently, the United States' CDC advised of increased paediatric iGAS disease in several states, including Colorado, Minnesota, and Texas (11-13), and the Pan American Health Organization (PAHO) published an informative note urging member countries to remain watchful for iGAS cases after several were identified in Uruguay ( 14).In Canada, there was an increase in the number of iGAS isolates submitted to NML in 2022 in comparison to 2021.Though the total yearly count did not exceed the highest totals collected pre-pandemic (years 2018 and 2019), there was a large increase in isolates collected in 2022-Q4, including in children.The WHO indicated that the increase in iGAS infections may be due to increased population mixing following a period of reduced circulation of GAS during the COVID-19 pandemic, and increased circulation of respiratory viruses (3); respiratory viruses and viral co-infections are associated with GAS infections and may increase the risk of invasive disease (3,15).Though our current study is unable to provide any Canadian data on viral co-infections with iGAS, several studies, including those in France, the United Kingdom, and the United States, reported increased rates of viral infection prior to or concurrent with iGAS infections (12,16,17).Associated viruses included influenza, respiratory syncytial virus, SARS-CoV-2 pandemic virus, human metapneumovirus, and rhinovirus (12,16,17).
Of note, countries reporting an increase in paediatric iGAS disease in late 2022 universally identified emm types 1 and 12 as the predominant cause of cases (12,13,(18)(19)(20)(21).In Canada, prevalence of emm1 was decreasing considerably going into the COVID-19 pandemic and was virtually non-existent in 2021 (0.5% of collected isolates).Though emm1 counts remained relatively low at the beginning of 2022, the prevalence did increase in Canada in Q4, as was seen in other countries.Almost half of emm1 isolates tested in 2022 were the M1 UK lineage originally described by Lynskey et al., as associated with hyperproduction of the SpeA exotoxin (7).Belgium, Netherlands, and the

Percent of all isolates
Year (number of isolates tested) United Kingdom have also noted high rates (~75%) of the M1 UK lineage in 2022 (22)(23)(24).Emm12 has similarly been associated with toxigenic lineages; this type has previously been linked with outbreaks of scarlet fever, with associated lineages possessing exotoxin SpeC and superantigen SSA, as well as antimicrobial resistance (25).Prior to 2022, prevalence of emm12 was decreasing significantly in Canada.A large increase in prevalence in 2022-Q4 (just over 13% of all isolates collected), resulted in an increase to ~6% overall in 2022.Little antimicrobial resistance was seen in emm12 during that time.Studies in the United States (Colorado, Minnesota, Texas) also did not identify any resistance during their late 2022 increases of emm12 (12,13).In Portugal, the 2022 iGAS increase was characterized by emm12 isolates with high genomic diversity, with no expansion of a particular lineage (20).Further genomic characterization of emm12 isolates in Canada would be useful to identify toxin profiles and potential outbreak lineages.
The most common emm type collected in Canada since 2020 has been emm49.At the time of writing our previous annual report in 2020 (2), emm49 was not common in the literature as a frequent or emerging type.However, more recently, a study from the United States identified emm49 as increasingly associated with antimicrobial resistance.Li et al. have identified a macrolide and lincosamide-resistant sublineage of emm49 that has rapidly expanded in the state of Maryland to become the dominant lineage (26).A Spanish study also noted the emergence of emm49 in late 2022 after previously being rarely detected in the country.These isolates differed from the American lineage in that they demonstrated resistance to only tetracycline (21).Though antimicrobial resistance in emm49 was rarely detected in Canada in 2021 and 2022 (<2% erythromycin resistance), it will be important to monitor for the emergence of drug-resistant clones.
Streptococcus pyogenes remains susceptible to penicillin, the first-line antimicrobial treatment for iGAS infections, however, resistance to erythromycin (a second-line therapy) continues to increase in Canada.In 2021 and 2022, commonly collected emm types in Canada with high levels (>40%) of erythromycin resistance were similar to those reported in 2020, including emm11, emm77, emm83, and emm92 (2).Of these, emm83 and emm92 demonstrated significant increases over the 2018 to 2022 time period.Similar studies from other countries confirm that these emm types demonstrate resistance elsewhere, such as Spain (emm11, emm77) and the United States (emm11, emm83, emm92) (26,27).Of note is emm92, which was identified in West Virginia, United States, as an emm type with uniform resistance to macrolides/lincosamides that is disproportionately affecting patients with a history of intravenous drug use (28).In Canada, iGAS disease outbreaks often occur in at-risk groups, such as persons experiencing homelessness or those who abuse substances, closed populations such as long-term care facilities, and Indigenous communities (29,30); it will be of significant concern if drug-resistant emm92 continues to expand in Canada into vulnerable populations.

Limitations
Caution should be exercised when interpreting the data presented in this report, as the overall interpretation of the results is limited to only isolates available for testing.Only a subset of the laboratory isolates from each province may have been submitted for testing, therefore, this report does not reflect the true incidence or rates of disease in Canada.The representativeness of the proportions of isolates submitted to NML for testing as compared to the CNDSS are presented in Appendix, Table S5.Not all provinces and territories report line list data to CNDSS, which means that only aggregated data are available at the national level.Therefore, CNDSS data and NML laboratory data are presented differently in terms of age grouping.

Figure S1 :
Figure S8: Prevalence of the ten most common invasive Streptococcus pyogenes emm types collected from Western Canada in A) 2021 and B) 2022 Figure S9: Prevalence of the ten most common invasive Streptococcus pyogenes emm types collected from Central Canada in A) 2021 and B) 2022 Figure S10: Prevalence of the ten most common invasive Streptococcus pyogenes emm types collected from Eastern Canada in A) 2021 and B) 2022 Figure S11: Prevalence of the ten most common invasive Streptococcus pyogenes emm types collected from Northern Canada in A) 2021 and B) 2022Table S2: Antimicrobial-resistant invasive Streptococcus pyogenes isolates by year, 2018-2022 Figure S12: Percentage of macrolide and lincosamide resistant Streptococcus pyogenes isolates collected in 2021, by emm type Figure S13: Percentage of macrolide and lincosamide resistant Streptococcus pyogenes isolates collected in 2022, by emm type Table S3: Percentage of macrolide and lincosamide resistant Streptococcus pyogenes isolates collected in 2021, by emm type Table S4: Percentage of macrolide and lincosamide resistant Streptococcus pyogenes isolates collected in 2021, by emm type Table S5: Number of invasive Streptococcus pyogenes isolates types by the National Microbiology Laboratory (NML) in comparison to the total number of cases reported to the Canadian Notifiable Diseases Surveillance System (CNDSS) in 2021, by patient age group

Table 1 :
Number of invasive Streptococcus pyogenes isolates collected by each Canadian province/region, 2021-2022 a Includes isolates from New Brunswick, Prince Edward Island, Nova Scotia, and Newfoundland and Labrador b Includes isolates from Yukon, Northwest Territories, and NunavutIsolate testing The most predominant emm type overall in 2021 and 2022 was emm49, at 21.5% (n=468) and 16.9% (n=444), respectively, representing a significant increase in prevalence since 2018 (from 3.1%, n=99; p<0.0001) (Figure3).
for 19.0% and 24.4%.Of the isolates for which sex information was available, isolates from male patients represented 61.8% and 61.7% of isolates in 2021 and 2022, respectively.Blood was the predominant clinical isolation site, accounting for 69.3% of isolates collected in 2021 and 70.5% in 2022.Additional information on specimen source by age and emm type can be found in Appendix, FiguresS1-S5.Figure 2: Number of invasive Streptococcus pyogenes isolates collected each quarter a for children younger than 15 years and patients 15 years of age and older b , 2018-2022 Abbreviation: Qtr, quater a Qtr1, January to March; Qtr 2, April to June; Qtr 3, July to September; Qtr 4, October to December; all month ranges are inclusive b Yearly isolate counts include those where no age was given a Cases per 100,000 population CCDR • May 2024 • Vol.50 No. 5 UK .Another type of interest is emm12, which did not demonstrate a significant trend from 2018 to 2022; however, emm12 decreased significantly from 4.5% (n=145) in 2018 to 1.0% (n=22) in 2021 (p<0.0001),beforesignificantlyrisingback up to 5.8% (n=151) in 2022 (p<0.0001).Counts of emm1 and emm12 saw a particular re-emergence in late 2022, together accounting for almost 25% of isolates collected in Q4 (Figure4).In 2021, the most common emm type from children <15 years of age was emm49 (28.2%, n=24).Emm49 dropped to the third most common type in this age group in 2022, instead replaced by emm12 (25.8%, n=49) and emm1 (24.2%, n=46) (Appendix, FigureS6).In patients aged 15 years and older, emm49 (21.3%, n=442) and emm76 (10.0%, n=207) were most common in 2021.In 2022, emm49 (17.0%, n=412) was also the most common type in the age group, followed by emm74 (9.7%, n=236) and emm82 (9.5%, n=230) (Appendix, FigureS7).Upon request, NML provides assistance to provincial and territorial public health laboratories for iGAS outbreak/case cluster investigations (including non-invasive isolates from screening) and jurisdictional emm increases.During 2021, NML assisted in four outbreak investigations from various jurisdictions, Antimicrobial resistance among iGAS isolates remained low in 2021-2022 (Figure6, Appendix, TableS2).Erythromycin resistance increased significantly from 9.8% in 2018 to 14.1% in 2022 (p<0.0001), while chloramphenicol resistance decreased significantly from 1.2% to 0.3% (p<0.0001).Clindamycin resistance remained relatively stable over the study period (2.9%-4.8%).There was no resistance observed to penicillin or

Table S1 :
the number of isolates collected was low in 2021, iGAS counts increased in 2022, particularly in the latter part of the year.Emm49 remained the most common type collected in Canada for 2021 and 2022; however, emm1 and emm12 began to rapidly increase in prevalence in the final quarter of 2022.As iGAS counts continue to rise following the COVID-19 pandemic, continued surveillance is imperative to monitor emm types and antimicrobial resistance in Canada.Enhancing surveillance to include linked epidemiological and laboratory data would improve our knowledge and interpretation of how iGAS emm types and antimicrobial resistance patterns affect at-risk groups in Canada.Annual incidence rates of invasive Streptococcus pyogenes in Canada by age group, 2011-2021

Table S2 :
Antimicrobial-resistant invasive Streptococcus pyogenes isolates by year, 2018-2022 Figure S12: Percentage of macrolide and lincosamide resistant Streptococcus pyogenes isolates collected in 2021, by emm type Figure S13: Percentage of macrolide and lincosamide resistant Streptococcus pyogenes isolates collected in 2022, by emm type Table S3: Percentage of macrolide and lincosamide resistant Streptococcus pyogenes isolates collected in 2021, by emm type Table S4: Percentage of macrolide and lincosamide resistant Streptococcus pyogenes isolates collected in 2021, by emm type Table S5: Number of invasive Streptococcus pyogenes isolates types by the National Microbiology Laboratory (NML) in comparison to the total number of cases reported to the Canadian Notifiable Diseases Surveillance System (CNDSS) in 2021, by patient age group